小柯机器人

科学家绘制出小鼠胚胎发育的动态染色质图谱
2020-08-02 23:52

美国加州大学圣迭戈分校任兵等研究人员合作绘制出小鼠胚胎发育的动态染色质图谱。2020年7月29日出版的《自然》杂志发表了这项成果。

研究人员系统地检查了发育小鼠胚胎中染色质的状态和可及性。在72个不同组织阶段,研究人员总共进行了1128次染色质免疫沉淀测序(ChIP–seq)进行组蛋白修饰分析,并使用测序(ATAC–seq)进行了132次染色质转座酶可及性分析。研究人员使用整合分析开发了一套统一的染色质状态注释,可推断动态增强子和关键转录调节子的身份,并表征发育基因调控过程中染色质状态与可及性之间的关系。
 
研究人员还利用这些数据将增强子与推定的靶基因联系起来,并证明了与人类疾病相关序列变异的组织特异性富集。小鼠ENCODE数据集为生物医学研究人员提供了资源,并获得了哺乳动物胚胎发育过程中染色质动态的最全面视图。
 
据悉,ENCODE(Encyclopedia of DNA Elements)项目为哺乳动物的发育建立了基因组资源,从受孕后10.5天到出生,在8个发育阶段对多种小鼠组织进行了分析,包括转录组,甲基化组和染色质状态。
 
附:英文原文

Title: An atlas of dynamic chromatin landscapes in mouse fetal development

Author: David U. Gorkin, Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang, Ah Young Lee, Bin Li, Joshua Chiou, Andre Wildberg, Bo Ding, Bo Zhang, Mengchi Wang, J. Seth Strattan, Jean M. Davidson, Yunjiang Qiu, Veena Afzal, Jennifer A. Akiyama, Ingrid Plajzer-Frick, Catherine S. Novak, Momoe Kato, Tyler H. Garvin, Quan T. Pham, Anne N. Harrington, Brandon J. Mannion, Elizabeth A. Lee, Yoko Fukuda-Yuzawa, Yupeng He, Sebastian Preissl, Sora Chee, Jee Yun Han, Brian A. Williams, Diane Trout, Henry Amrhein, Hongbo Yang, J. Michael Cherry, Wei Wang, Kyle Gaulton, Joseph R. Ecker, Yin Shen, Diane E. Dickel, Axel Visel, Len A. Pennacchio, Bing Ren

Issue&Volume: 2020-07-29

Abstract: The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP–seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC–seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.

DOI: 10.1038/s41586-020-2093-3

Source: https://www.nature.com/articles/s41586-020-2093-3

Nature:《自然》,创刊于1869年。隶属于施普林格·自然出版集团,最新IF:43.07
官方网址:http://www.nature.com/
投稿链接:http://www.nature.com/authors/submit_manuscript.html


本期文章:《自然》:Online/在线发表

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